Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1

Gao, Boliang; Jin, Min; Li, Li; Qu, Wu; Zeng, Runying

doi:10.3389/fmicb.2017.00600

Cited by 38 publications

(39 citation statements)

References 67 publications

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“…According to the annotation results from the CAZy database, the ORFs of 43 auxiliary CAZyme genes are mostly affiliated with glycoside hydrolase (GH) and glycosyl transferase (GT) (Figure 6b), implying the importance of these functional genes for the degradation of marine organic carbons. Actually, complex carbohydrates, such as starch, xylan, cellulose, chitin, alginate, mannan, and pectin, are major components of algae cell walls and microbial intercellular spaces, and they are highly difficult to degrade [75]. Notably, in viruses, multiple genes encode CAZymes, such as hydrolysis enzymes and auxiliary enzymes, which are necessary for the degradation of various extracellular polymeric substance (EPSs) [76], indicating viral abilities in the biolysis of complex polysaccharides during bloom events.…”

Section: Functional Prediction Of Algal Bloom Sample Viromesmentioning

confidence: 99%

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

Cai

Zuo

et al. 2020

Microorganisms

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Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.

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Section: Functional Prediction Of Algal Bloom Sample Viromesmentioning

confidence: 99%

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

Cai

Zuo

et al. 2020

Microorganisms

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“…Some members of the phyla Chloro exi (OTU10701, 16075, and 12101) and Acidobacteria (OTU2963) are also photoautotrophic bacteria [41]. In addition, the families Flavobacteriaceae (OTU11086) [50,51], Flammeovirgaceae (OTU6475) [52,53], and Draconibacteriaceae (OTU11996) [54,55] and the order Xanthomonadales (OTU5104 and 11887) [56] degrade stable polysaccharides into active monosaccharides.…”

Section: Discussionmentioning

confidence: 99%

High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

Qu¹,

Gao²,

Wu³

et al. 2020

Preprint

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Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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“…Hou et al reported the expression and characterisation of a novel thermostable and pH-stable β-agarase AgaP4383 from the deep-sea bacterium Flammeovirga pacifica WPAGA1 [49]. Phenotypic and genomic analyses revealed that F. pacifica WPAGA1 is capable of degrading and metabolising complex polysaccharides and can grow on the red alga Gracilaria lemaneiformis as a sole carbon source [64,65], and that AgaP4383 exhibits endolytic activity on agar degradation, producing neoagarotetraose and neoagarohexaose as the final products. AgaP4383 also exhibits good thermostability, with no loss of activity after incubation at 50 • C for 10 h [63].…”

Section: Deep-sea Thermophilic Enzymesmentioning

confidence: 99%

Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

et al. 2019

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The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.Nearly three-quarters of the Earth's surface area is covered by ocean, the average depth of which is 3800 m, implying that the vast majority of our planet comprises deep-sea environments. The deep sea is one of the most mysterious and unexplored environments on the Earth, and it supports diverse microbial communities that play important roles in biogeochemical cycles [1]. The deep sea is also recognised as an extreme environment, as it is characterised by the absence of sunlight and the presence of predominantly low temperatures and high hydrostatic pressures, and these environmental conditions become even more challenging in particular habitats, such as deep-sea hydrothermal vents with their extremely high temperatures of >400 • C, deep hypersaline anoxic basins (DHABs) with their extremely high salinities and abysses of up to 11 km depth with their extremely high pressures.Deep-sea extremophiles are living organisms that can survive and proliferate in deep-sea environments that have extreme physical (pressure and temperature) and geochemical (pH, salinity and redox potential) conditions that are lethal to other organisms. The majority of deep-sea extremophiles belong to the prokaryotes, which are microorganisms in the domains of Archaea and Bacteria [2,3].These extremophilic microorganisms are functionally diverse and widely distributed in taxonomy [4], and they are classified into thermophiles (55 • C to 121 • C), psychrophiles (−2 • C to 20 • C), halophiles (2-5 M NaCl or KCl), piezophiles (>500 atmospheres), alkalophiles (pH > 8), acidophiles (pH < 4) and metalophiles (high concentrations of metals, e.g., copper, zinc, cadmium and arsenic) according to the extreme environments in which they grow and the extreme conditions they can tolerate. Ma...

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Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1

Cited by 38 publications

References 67 publications

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

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